Rapid large-scale prokaryote pan genome analysis
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Finds SNP sites from a multi-FASTA alignment file
A tool to circularize genome assemblies
Antimicrobial Resistance Identification By Assembly
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Pathogen NGS Documentary
Get assembly statistics from FASTA and FASTQ files
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Python3 scripts to manipulate FASTA and FASTQ files
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Improve the quality of a denovo assembly by scaffolding and gap filling
de novo virus assembler of Illumina paired reads
Predict plasmids from uncorrected long read data
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Assembling the cause of phenotypes and genotypes from NGS data
Multilocus sequence typing by blast using the schemes from PubMLST
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